From: Sean L. <mag...@ho...> - 2010-09-13 20:55:11
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Hi PyMOLers, I think there is a bug in PyMOL regarding the "set cartoon_transparency" setting. According to the PyMOL-Wiki, the arguments are: set cartoon_transparency, value, selection where the "value" ranges from 0.0-1.0 and the selection is optional. However, selections that are not entire objects does not seem to function properly as in other similar settings (e.g. set transparency). I tried the following test: fetch 1bna hide all show cartoon set cartoon_transparency, 0.5, c. a #It should say "cartoon_transparency set for 280 atoms in object "1bna" ray However, after ray tracing, no part of the object is shown as being transparent. Of course, when you leave out the optional "selection" then everything behaves as expected. I hope that this behaviour gets corrected for the next build. Thanks in advance! Sean |
From: Jason V. <jas...@sc...> - 2010-09-14 16:35:49
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Hi Sean, Thanks for posting this. I also encountered and took note of this bug when making the figures for your script. Cheers, -- Jason On Mon, Sep 13, 2010 at 4:55 PM, Sean Law <mag...@ho...> wrote: > Hi PyMOLers, > > I think there is a bug in PyMOL regarding the "set cartoon_transparency" > setting. According to the PyMOL-Wiki, the arguments are: > > set cartoon_transparency, value, selection > > where the "value" ranges from 0.0-1.0 and the selection is optional. > However, selections that are not entire objects does not seem to function > properly as in other similar settings (e.g. set transparency). I tried the > following test: > > fetch 1bna > hide all > show cartoon > set cartoon_transparency, 0.5, c. a > #It should say "cartoon_transparency set for 280 atoms in object "1bna" > ray > > However, after ray tracing, no part of the object is shown as being > transparent. Of course, when you leave out the optional "selection" then > everything behaves as expected. I hope that this behaviour gets corrected > for the next build. > > Thanks in advance! > > Sean > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing > http://p.sf.net/sfu/novell-sfdev2dev > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |